rs17066879

Positions:

• chr18-60397626-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658928.1(ENSG00000285681):​n.156+68281A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,076 control chromosomes in the GnomAD database, including 2,510 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.18 (2510 hom., cov: 32)
• Consequence: ENST00000658928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000658928.1	n.156+68281A>T		intron_variant, non_coding_transcript_variant
	ENST00000650201.1	n.113+68281A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27122 AN: 151958 Hom.: 2500 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0372

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.135

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.159

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.179 AC: 27157 AN: 152076 Hom.: 2510 Cov.: 32 AF XY: 0.174 AC XY: 12900 AN XY: 74336

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0375

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.157

Alfa AF: 0.185 Hom.: 350

Bravo AF: 0.178

Asia WGS AF: 0.0940 AC: 325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17066879; hg19: chr18-58064859;